Erwinia (oligotyping)
Load packages, paths, functions
# Load main packages, paths and custom functions
source("../../../source/main_packages.R")
source("../../../source/paths.R")
source("../../../source/functions.R")
# Load supplementary packages
packages <- c("RColorBrewer", "ggpubr", "cowplot", "Biostrings", "openxlsx", "kableExtra")
invisible(lapply(packages, require, character.only = TRUE))Preparation
Tables preparation
Seqtab
# move to oligotyping directory
setwd(paste0(path_oligo,"/erwinia/oligotyping_Erwinia_sequences-c8-s1-a0.0-A0-M10"))
# load the matrix count table
matrix_count <- read.table("MATRIX-COUNT.txt", header = TRUE) %>% t()
# arrange it
colnames(matrix_count) <- matrix_count[1,]
matrix_count <- matrix_count[-1,]
matrix_count <- matrix_count %>% as.data.frame()
# print it
matrix_count %>%
kbl() %>%
kable_paper("hover", full_width = F)| CTC1 | CTC10 | CTC11 | CTC12 | CTC13 | CTC14 | CTC15 | CTC2 | CTC3 | CTC4 | CTC5 | CTC6 | CTC7 | CTC9 | NP27 | NP34 | NP36 | S146 | S164 | S165 | S166 | S167 | S20 | S21 | S22 | S24 | S30 | S31 | S32 | S33 | S34 | S35 | S36 | S37 | S38 | S44 | S45 | S46 | S48 | S49 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| AAGACTTA | 2561 | 530 | 3566 | 332 | 1919 | 152 | 2825 | 2145 | 2268 | 147 | 11 | 3121 | 27 | 622 | 6 | 1 | 1 | 1 | 2 | 4 | 1 | 2 | 5 | 1 | 2 | 7 | 4069 | 4534 | 1857 | 3578 | 692 | 8 | 2513 | 377 | 19 | 26 | 46 | 7 | 32 | 8 |
| TGAGTCGA | 499 | 108 | 918 | 74 | 418 | 34 | 570 | 441 | 412 | 28 | 0 | 616 | 6 | 149 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 2 | 0 | 1 | 582 | 648 | 208 | 766 | 69 | 0 | 448 | 84 | 0 | 3 | 18 | 1 | 0 | 4 |
| AAGACTTG | 536 | 123 | 1017 | 94 | 402 | 45 | 588 | 442 | 386 | 27 | 3 | 760 | 7 | 123 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 15 | 13 | 2 | 3 | 2 | 0 | 4 | 1 | 0 | 0 | 0 | 1 | 0 | 0 |
| TGAGTCGG | 101 | 21 | 247 | 25 | 90 | 10 | 99 | 94 | 72 | 2 | 1 | 158 | 1 | 35 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 2 | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| TGAGTCGT | 28 | 4 | 63 | 9 | 36 | 3 | 35 | 24 | 19 | 1 | 0 | 41 | 2 | 6 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| TGAGCCGA | 10 | 3 | 24 | 4 | 10 | 3 | 18 | 12 | 4 | 1 | 0 | 10 | 0 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 2 | 1 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| AAGACCTA | 10 | 0 | 9 | 1 | 3 | 0 | 0 | 9 | 8 | 0 | 0 | 6 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| AGGACTTA | 2 | 2 | 6 | 0 | 3 | 1 | 10 | 5 | 0 | 1 | 0 | 5 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 6 | 2 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| AAGGCTTA | 7 | 1 | 4 | 0 | 5 | 0 | 5 | 2 | 3 | 0 | 0 | 6 | 0 | 5 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 2 | 0 | 0 | 3 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
Taxonomy
# move to oligotyping directory
setwd(paste0(path_oligo,"/erwinia/oligotyping_Erwinia_sequences-c8-s1-a0.0-A0-M10"))
# load the fasta table
fasta <- readDNAStringSet("OLIGO-REPRESENTATIVES.fasta")
# arrange it
fasta <- fasta %>% as.data.frame()
colnames(fasta) <- "seq"
fasta$oligotype <- rownames(fasta)
fasta <- fasta %>% dplyr::select(-c(seq))
# print it
fasta %>%
kbl() %>%
kable_paper("hover", full_width = F)| oligotype | |
|---|---|
| AAGACTTA | AAGACTTA |
| TGAGTCGA | TGAGTCGA |
| AAGACTTG | AAGACTTG |
| TGAGTCGG | TGAGTCGG |
| TGAGTCGT | TGAGTCGT |
| TGAGCCGA | TGAGCCGA |
| AAGACCTA | AAGACCTA |
| AGGACTTA | AGGACTTA |
| AAGGCTTA | AAGGCTTA |
Change oligotype name by oligotype / MED nodes in the matrix count
# Reference file
## move to tsv directory
setwd(path_tsv)
## load the reference table
ref_oligo_med2 <- read.table("2B_REF_info_erwinia.tsv", sep="\t", header = TRUE)
## select only the 3 oligotypes of Erwinia
ref_oligo_med2 <- ref_oligo_med2[!is.na(ref_oligo_med2$oligotype),]
## change order of columns
ref_oligo_med2 <- ref_oligo_med2 %>% select(c(seq, oligotype, MED_node_frequency_size, OLIGO_oligotype_frequency_size))
## create a column with reference name (will be used in plots)
ref_oligo_med2$ref <- paste0("oligotype_", ref_oligo_med2$OLIGO_oligotype_frequency_size, " / node_", ref_oligo_med2$MED_node_frequency_size)
## create a copy of fasta
fasta2 <- fasta
# Matrix count
## create an oligotype column in the matrix count
matrix_count$oligotype <- rownames(matrix_count)
## change order of columns
matrix_count <- matrix_count %>% dplyr::select(c(oligotype, everything()))
## merge the matrix count and the reference dataframe
matrix_count2 <- matrix_count %>% merge(ref_oligo_med2 %>% dplyr::select(-c(seq)), by="oligotype")
## change order of columns
matrix_count2 <- matrix_count2 %>% dplyr::select(c(oligotype, MED_node_frequency_size, OLIGO_oligotype_frequency_size, ref, everything()))
## change rownames
rownames(matrix_count2) <- matrix_count2$ref
## change order of columns
matrix_count2 <- matrix_count2 %>% dplyr::select(-c(oligotype, ref, MED_node_frequency_size, OLIGO_oligotype_frequency_size))
## print it
matrix_count2 %>%
kbl() %>%
kable_paper("hover", full_width = F)| CTC1 | CTC10 | CTC11 | CTC12 | CTC13 | CTC14 | CTC15 | CTC2 | CTC3 | CTC4 | CTC5 | CTC6 | CTC7 | CTC9 | NP27 | NP34 | NP36 | S146 | S164 | S165 | S166 | S167 | S20 | S21 | S22 | S24 | S30 | S31 | S32 | S33 | S34 | S35 | S36 | S37 | S38 | S44 | S45 | S46 | S48 | S49 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| oligotype_AAGACTTA (40) | size:38025 / node_N0798 (40) | size:38213 | 2561 | 530 | 3566 | 332 | 1919 | 152 | 2825 | 2145 | 2268 | 147 | 11 | 3121 | 27 | 622 | 6 | 1 | 1 | 1 | 2 | 4 | 1 | 2 | 5 | 1 | 2 | 7 | 4069 | 4534 | 1857 | 3578 | 692 | 8 | 2513 | 377 | 19 | 26 | 46 | 7 | 32 | 8 |
| oligotype_AAGACTTG (22) | size:4594 / node_N0802 (22) | size:4627 | 536 | 123 | 1017 | 94 | 402 | 45 | 588 | 442 | 386 | 27 | 3 | 760 | 7 | 123 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 15 | 13 | 2 | 3 | 2 | 0 | 4 | 1 | 0 | 0 | 0 | 1 | 0 | 0 |
| oligotype_TGAGTCGA (29) | size:7110 / node_N0311 (30) | size:8523 | 499 | 108 | 918 | 74 | 418 | 34 | 570 | 441 | 412 | 28 | 0 | 616 | 6 | 149 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 2 | 0 | 1 | 582 | 648 | 208 | 766 | 69 | 0 | 448 | 84 | 0 | 3 | 18 | 1 | 0 | 4 |
## edit the fasta dataframe
fasta2 <- fasta2 %>% merge(ref_oligo_med2 %>% dplyr::select(-c(seq)), by="oligotype")
rownames(fasta2) <- fasta2$ref
fasta2 <- fasta2 %>% dplyr::select(-c(MED_node_frequency_size, OLIGO_oligotype_frequency_size, oligotype))
## print it
fasta2 %>%
kbl() %>%
kable_paper("hover", full_width = F)| ref | |
|---|---|
| oligotype_AAGACTTA (40) | size:38025 / node_N0798 (40) | size:38213 | oligotype_AAGACTTA (40) | size:38025 / node_N0798 (40) | size:38213 |
| oligotype_AAGACTTG (22) | size:4594 / node_N0802 (22) | size:4627 | oligotype_AAGACTTG (22) | size:4594 / node_N0802 (22) | size:4627 |
| oligotype_TGAGTCGA (29) | size:7110 / node_N0311 (30) | size:8523 | oligotype_TGAGTCGA (29) | size:7110 / node_N0311 (30) | size:8523 |
Metadata
Phyloseq object with oligotypes
# convert matrix_count into matrix and numeric
matrix_count <- matrix_count2 %>% as.matrix()
class(matrix_count) <- "numeric"
# phyloseq elements
OTU = otu_table(as.matrix(matrix_count), taxa_are_rows =TRUE)
TAX = tax_table(as.matrix(fasta2))
SAM = sample_data(metadata)
# phyloseq object
ps <- phyloseq(OTU, TAX, SAM)
ps## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 3 taxa and 40 samples ]
## sample_data() Sample Data: [ 40 samples by 13 sample variables ]
## tax_table() Taxonomy Table: [ 3 taxa by 1 taxonomic ranks ]
## [1] 49729
## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 3 taxa and 40 samples ]
## sample_data() Sample Data: [ 40 samples by 13 sample variables ]
## tax_table() Taxonomy Table: [ 3 taxa by 1 taxonomic ranks ]
Create new metadata with Percent
Load ps with all samples (for final plot)
Edit new metadata with Percent_erwinia
guide_italics <- guides(fill = guide_legend(label.theme = element_text(size = 16, face = "italic", colour = "Black", angle = 0)))
# add read depth in sample table of phyloseq object
sample_data(ps.filter)$Read_depth <- sample_sums(ps.filter)
# select Wolbachia
ps.erwinia <- ps.filter %>% subset_taxa(Genus=="Erwinia")
# add read depth of Wolbachia
sample_data(ps.filter)$Read_erwinia <- sample_sums(ps.erwinia)
sample_data(ps.filter) %>% colnames()## [1] "Sample" "Well" "Strain" "Field"
## [5] "Country" "Organ" "Species" "Individual"
## [9] "Individuals" "Date" "Run" "Control"
## [13] "Dna" "Species_italic" "Strain_italic" "Read_depth"
## [17] "is.neg" "Read_erwinia"
## [1] "Sample" "Well" "Strain" "Field"
## [5] "Country" "Organ" "Species" "Individual"
## [9] "Individuals" "Date" "Run" "Control"
## [13] "Dna" "Species_italic" "Strain_italic" "Read_depth"
## [17] "is.neg"
# add percent of Wolbachia
sample_data(ps.filter)$Percent_erwinia <- sample_data(ps.filter)$Read_erwinia / sample_data(ps.filter)$Read_depth
# round the percent of Wolbachia at 2 decimals
sample_data(ps.filter)$Percent_erwinia <- sample_data(ps.filter)$Percent_erwinia %>% round(2)
# extract metadata table
test <- data.frame(sample_data(ps.filter))
# merge this metadata table with the other
new.metadata <- data.frame(sample_data(ps)) %>% merge(test %>% dplyr::select(c(Sample, Read_depth, Read_erwinia, Percent_erwinia)), by="Sample")
new.metadata <- test[new.metadata$Sample %in% sample_names(ps),]
rownames(new.metadata) <- new.metadata$Sample
# print it
new.metadata %>%
kbl() %>%
kable_paper("hover", full_width = F)| Sample | Well | Strain | Field | Country | Organ | Species | Individual | Individuals | Date | Run | Control | Dna | Species_italic | Strain_italic | Read_depth | is.neg | Read_erwinia | Percent_erwinia | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CTC1 | CTC1 | G5 | Laboratory - Slab TC (Wolbachia -) | Lab | France | Whole | Culex quinquefasciatus | N/A | 0 | 09/03/2018 | run2 | True sample | 99 | italic(“Culex quinquefasciatus”) | paste(“Laboratory - Slab TC (”, italic(“Wolbachia”), “-)”) | 29779 | FALSE | 3769 | 0.13 |
| CTC10 | CTC10 | D6 | Laboratory - Slab TC (Wolbachia -) | Lab | France | Whole | Culex quinquefasciatus | N/A | 0 | 09/03/2018 | run2 | True sample | 77 | italic(“Culex quinquefasciatus”) | paste(“Laboratory - Slab TC (”, italic(“Wolbachia”), “-)”) | 2609 | FALSE | 799 | 0.31 |
| CTC11 | CTC11 | E6 | Laboratory - Slab TC (Wolbachia -) | Lab | France | Whole | Culex quinquefasciatus | N/A | 0 | 09/03/2018 | run2 | True sample | 99 | italic(“Culex quinquefasciatus”) | paste(“Laboratory - Slab TC (”, italic(“Wolbachia”), “-)”) | 13874 | FALSE | 5878 | 0.42 |
| CTC12 | CTC12 | F6 | Laboratory - Slab TC (Wolbachia -) | Lab | France | Whole | Culex quinquefasciatus | N/A | 0 | 09/03/2018 | run2 | True sample | 87 | italic(“Culex quinquefasciatus”) | paste(“Laboratory - Slab TC (”, italic(“Wolbachia”), “-)”) | 1146 | FALSE | 542 | 0.47 |
| CTC13 | CTC13 | G6 | Laboratory - Slab TC (Wolbachia -) | Lab | France | Whole | Culex quinquefasciatus | N/A | 0 | 09/03/2018 | run2 | True sample | 99 | italic(“Culex quinquefasciatus”) | paste(“Laboratory - Slab TC (”, italic(“Wolbachia”), “-)”) | 18035 | FALSE | 2898 | 0.16 |
| CTC14 | CTC14 | H6 | Laboratory - Slab TC (Wolbachia -) | Lab | France | Whole | Culex quinquefasciatus | N/A | 0 | 09/03/2018 | run2 | True sample | 101 | italic(“Culex quinquefasciatus”) | paste(“Laboratory - Slab TC (”, italic(“Wolbachia”), “-)”) | 1708 | FALSE | 253 | 0.15 |
| CTC15 | CTC15 | I6 | Laboratory - Slab TC (Wolbachia -) | Lab | France | Whole | Culex quinquefasciatus | N/A | 0 | 09/03/2018 | run2 | True sample | 99 | italic(“Culex quinquefasciatus”) | paste(“Laboratory - Slab TC (”, italic(“Wolbachia”), “-)”) | 23180 | FALSE | 4159 | 0.18 |
| CTC2 | CTC2 | H5 | Laboratory - Slab TC (Wolbachia -) | Lab | France | Whole | Culex quinquefasciatus | N/A | 0 | 09/03/2018 | run2 | True sample | 99 | italic(“Culex quinquefasciatus”) | paste(“Laboratory - Slab TC (”, italic(“Wolbachia”), “-)”) | 30692 | FALSE | 3181 | 0.10 |
| CTC3 | CTC3 | I5 | Laboratory - Slab TC (Wolbachia -) | Lab | France | Whole | Culex quinquefasciatus | N/A | 0 | 09/03/2018 | run2 | True sample | 99 | italic(“Culex quinquefasciatus”) | paste(“Laboratory - Slab TC (”, italic(“Wolbachia”), “-)”) | 39920 | FALSE | 3184 | 0.08 |
| CTC4 | CTC4 | J5 | Laboratory - Slab TC (Wolbachia -) | Lab | France | Whole | Culex quinquefasciatus | N/A | 0 | 09/03/2018 | run2 | True sample | 29 | italic(“Culex quinquefasciatus”) | paste(“Laboratory - Slab TC (”, italic(“Wolbachia”), “-)”) | 2139 | FALSE | 207 | 0.10 |
| CTC5 | CTC5 | K5 | Laboratory - Slab TC (Wolbachia -) | Lab | France | Whole | Culex quinquefasciatus | N/A | 0 | 09/03/2018 | run2 | True sample | 99 | italic(“Culex quinquefasciatus”) | paste(“Laboratory - Slab TC (”, italic(“Wolbachia”), “-)”) | 15789 | FALSE | 15 | 0.00 |
| CTC6 | CTC6 | L5 | Laboratory - Slab TC (Wolbachia -) | Lab | France | Whole | Culex quinquefasciatus | N/A | 0 | 09/03/2018 | run2 | True sample | 99 | italic(“Culex quinquefasciatus”) | paste(“Laboratory - Slab TC (”, italic(“Wolbachia”), “-)”) | 19753 | FALSE | 4739 | 0.24 |
| CTC9 | CTC9 | C6 | Laboratory - Slab TC (Wolbachia -) | Lab | France | Whole | Culex quinquefasciatus | N/A | 0 | 09/03/2018 | run2 | True sample | 67 | italic(“Culex quinquefasciatus”) | paste(“Laboratory - Slab TC (”, italic(“Wolbachia”), “-)”) | 4980 | FALSE | 948 | 0.19 |
| NP14 | NP14 | K4 | Field - Guadeloupe | Field | Guadeloupe | Ovary | Aedes aegypti | 1a | 0 | N/A | run3 | True sample | 19 | italic(“Aedes aegypti”) | Field-Guadeloupe | 7973 | FALSE | 0 | 0.00 |
| NP2 | NP2 | K3 | Field - Guadeloupe | Field | Guadeloupe | Ovary | Culex quinquefasciatus | 1c | 0 | N/A | run3 | True sample | 89 | italic(“Culex quinquefasciatus”) | Field-Guadeloupe | 648335 | FALSE | 0 | 0.00 |
| NP20 | NP20 | E5 | Field - Guadeloupe | Field | Guadeloupe | Ovary | Aedes aegypti | 3a | 0 | N/A | run3 | True sample | 18 | italic(“Aedes aegypti”) | Field-Guadeloupe | 136 | FALSE | 0 | 0.00 |
| NP27 | NP27 | L5 | Field - Guadeloupe | Field | Guadeloupe | Whole | Culex quinquefasciatus | 7c | 0 | N/A | run3 | True sample | 30 | italic(“Culex quinquefasciatus”) | Field-Guadeloupe | 1234 | FALSE | 7 | 0.01 |
| NP29 | NP29 | B6 | Field - Guadeloupe | Field | Guadeloupe | Whole | Culex quinquefasciatus | 9c | 0 | N/A | run3 | True sample | 16 | italic(“Culex quinquefasciatus”) | Field-Guadeloupe | 203 | FALSE | 0 | 0.00 |
| NP30 | NP30 | C6 | Field - Guadeloupe | Field | Guadeloupe | Whole | Culex quinquefasciatus | 10c | 0 | N/A | run3 | True sample | 24 | italic(“Culex quinquefasciatus”) | Field-Guadeloupe | 228 | FALSE | 0 | 0.00 |
| NP34 | NP34 | G6 | Field - Guadeloupe | Field | Guadeloupe | Whole | Culex quinquefasciatus | 14c | 0 | N/A | run3 | True sample | 20 | italic(“Culex quinquefasciatus”) | Field-Guadeloupe | 95 | FALSE | 2 | 0.02 |
| NP35 | NP35 | H6 | Field - Guadeloupe | Field | Guadeloupe | Whole | Aedes aegypti | 7a | 0 | N/A | run3 | True sample | 84 | italic(“Aedes aegypti”) | Field-Guadeloupe | 196532 | FALSE | 0 | 0.00 |
| NP36 | NP36 | I6 | Field - Guadeloupe | Field | Guadeloupe | Whole | Aedes aegypti | 8a | 0 | N/A | run3 | True sample | 27 | italic(“Aedes aegypti”) | Field-Guadeloupe | 249 | FALSE | 1 | 0.00 |
| NP37 | NP37 | J6 | Field - Guadeloupe | Field | Guadeloupe | Whole | Aedes aegypti | 9a | 0 | N/A | run3 | True sample | 52 | italic(“Aedes aegypti”) | Field-Guadeloupe | 419340 | FALSE | 0 | 0.00 |
| NP38 | NP38 | K6 | Field - Guadeloupe | Field | Guadeloupe | Whole | Aedes aegypti | 10a | 0 | N/A | run3 | True sample | 62 | italic(“Aedes aegypti”) | Field-Guadeloupe | 282479 | FALSE | 0 | 0.00 |
| NP39 | NP39 | L6 | Field - Guadeloupe | Field | Guadeloupe | Whole | Aedes aegypti | 11a | 0 | N/A | run3 | True sample | 47 | italic(“Aedes aegypti”) | Field-Guadeloupe | 218684 | FALSE | 0 | 0.00 |
| NP41 | NP41 | B7 | Field - Guadeloupe | Field | Guadeloupe | Whole | Aedes aegypti | 13a | 0 | N/A | run3 | True sample | 93 | italic(“Aedes aegypti”) | Field-Guadeloupe | 247152 | FALSE | 0 | 0.00 |
| NP42 | NP42 | C7 | Field - Guadeloupe | Field | Guadeloupe | Whole | Aedes aegypti | 14a | 0 | N/A | run3 | True sample | 85 | italic(“Aedes aegypti”) | Field-Guadeloupe | 185157 | FALSE | 0 | 0.00 |
| NP43 | NP43 | D7 | Field - Guadeloupe | Field | Guadeloupe | Whole | Aedes aegypti | 15a | 0 | N/A | run3 | True sample | 104 | italic(“Aedes aegypti”) | Field-Guadeloupe | 239335 | FALSE | 0 | 0.00 |
| NP44 | NP44 | E7 | Field - Guadeloupe | Field | Guadeloupe | Whole | Aedes aegypti | 16a | 0 | N/A | run3 | True sample | 50 | italic(“Aedes aegypti”) | Field-Guadeloupe | 156879 | FALSE | 0 | 0.00 |
| NP5 | NP5 | B4 | Field - Guadeloupe | Field | Guadeloupe | Ovary | Culex quinquefasciatus | 2c | 0 | N/A | run3 | True sample | 66 | italic(“Culex quinquefasciatus”) | Field-Guadeloupe | 736159 | FALSE | 0 | 0.00 |
| NP8 | NP8 | E4 | Field - Guadeloupe | Field | Guadeloupe | Ovary | Culex quinquefasciatus | 3c | 0 | N/A | run3 | True sample | 92 | italic(“Culex quinquefasciatus”) | Field-Guadeloupe | 334799 | FALSE | 0 | 0.00 |
| S100 | S100 | K7 | Field - Camping Europe | Field | France | Ovary | Culex pipiens | GL1 | 1 | 30/05/2017 | run1 | True sample | 105 | italic(“Culex pipiens”) | Field-Camping~Europe | 52486 | FALSE | 0 | 0.00 |
| S102 | S102 | A8 | Field - Camping Europe | Field | France | Ovary | Culex pipiens | GL2 | 2 | 30/05/2017 | run1 | True sample | 14 | italic(“Culex pipiens”) | Field-Camping~Europe | 3456 | FALSE | 0 | 0.00 |
| S104 | S104 | C8 | Field - Camping Europe | Field | France | Ovary | Culex pipiens | GL5 | 5 | 30/05/2017 | run1 | True sample | 54 | italic(“Culex pipiens”) | Field-Camping~Europe | 52403 | FALSE | 0 | 0.00 |
| S105 | S105 | D8 | Field - Camping Europe | Field | France | Ovary | Culex pipiens | GL6 | 6 | 30/05/2017 | run1 | True sample | 103 | italic(“Culex pipiens”) | Field-Camping~Europe | 55577 | FALSE | 0 | 0.00 |
| S106 | S106 | E8 | Field - Camping Europe | Field | France | Ovary | Culex pipiens | GL7 | 7 | 30/05/2017 | run1 | True sample | 96 | italic(“Culex pipiens”) | Field-Camping~Europe | 33053 | FALSE | 0 | 0.00 |
| S107 | S107 | F8 | Field - Camping Europe | Field | France | Ovary | Culex pipiens | GL8 | 8 | 30/05/2017 | run1 | True sample | 65 | italic(“Culex pipiens”) | Field-Camping~Europe | 52154 | FALSE | 0 | 0.00 |
| S108 | S108 | G8 | Field - Camping Europe | Field | France | Ovary | Culex pipiens | GL9 | 9 | 30/05/2017 | run1 | True sample | 64 | italic(“Culex pipiens”) | Field-Camping~Europe | 55735 | FALSE | 0 | 0.00 |
| S109 | S109 | H8 | Field - Camping Europe | Field | France | Ovary | Culex pipiens | GL10 | 10 | 30/05/2017 | run1 | True sample | 55 | italic(“Culex pipiens”) | Field-Camping~Europe | 59023 | FALSE | 0 | 0.00 |
| S110 | S110 | I8 | Field - Camping Europe | Field | France | Ovary | Culex pipiens | GL11 | 0 | 30/05/2017 | run1 | True sample | 57 | italic(“Culex pipiens”) | Field-Camping~Europe | 57377 | FALSE | 0 | 0.00 |
| S121 | S121 | H1 | Field - Bosc | Field | France | Ovary | Culex pipiens | J26 | 22 | 28/06/2017 | run2 | True sample | 37 | italic(“Culex pipiens”) | Field-Bosc | 20361 | FALSE | 0 | 0.00 |
| S122 | S122 | I1 | Field - Bosc | Field | France | Ovary | Culex pipiens | J27 | 23 | 28/06/2017 | run2 | True sample | 52 | italic(“Culex pipiens”) | Field-Bosc | 9803 | FALSE | 0 | 0.00 |
| S123 | S123 | J1 | Field - Bosc | Field | France | Ovary | Culex pipiens | J28 | 24 | 28/06/2017 | run2 | True sample | 102 | italic(“Culex pipiens”) | Field-Bosc | 20130 | FALSE | 0 | 0.00 |
| S124 | S124 | K1 | Field - Bosc | Field | France | Ovary | Culex pipiens | J29 | 25 | 28/06/2017 | run2 | True sample | 69 | italic(“Culex pipiens”) | Field-Bosc | 18146 | FALSE | 0 | 0.00 |
| S126 | S126 | K6 | Field - Bosc | Field | France | Ovary | Culex pipiens | J30 | 26 | 28/06/2017 | run2 | True sample | 99 | italic(“Culex pipiens”) | Field-Bosc | 15235 | FALSE | 0 | 0.00 |
| S127 | S127 | B2 | Field - Bosc | Field | France | Ovary | Culex pipiens | J31 | 27 | 28/06/2017 | run2 | True sample | 38 | italic(“Culex pipiens”) | Field-Bosc | 24696 | FALSE | 0 | 0.00 |
| S128 | S128 | C2 | Field - Bosc | Field | France | Ovary | Culex pipiens | J32 | 28 | 28/06/2017 | run2 | True sample | 71 | italic(“Culex pipiens”) | Field-Bosc | 16305 | FALSE | 0 | 0.00 |
| S146 | S146 | I3 | Laboratory - Lavar | Lab | France | Ovary | Culex pipiens | MW52 | 29 | 29/08/2017 | run2 | True sample | 72 | italic(“Culex pipiens”) | Laboratory-Lavar | 25012 | FALSE | 1 | 0.00 |
| S147 | S147 | J3 | Laboratory - Lavar | Lab | France | Ovary | Culex pipiens | MW53 | 30 | 29/08/2017 | run2 | True sample | 56 | italic(“Culex pipiens”) | Laboratory-Lavar | 25171 | FALSE | 0 | 0.00 |
| S148 | S148 | K3 | Laboratory - Lavar | Lab | France | Ovary | Culex pipiens | MW54 | 31 | 29/08/2017 | run2 | True sample | 91 | italic(“Culex pipiens”) | Laboratory-Lavar | 14164 | FALSE | 0 | 0.00 |
| S150 | S150 | A4 | Laboratory - Lavar | Lab | France | Ovary | Culex pipiens | MW55 | 32 | 29/08/2017 | run2 | True sample | 43 | italic(“Culex pipiens”) | Laboratory-Lavar | 15081 | FALSE | 0 | 0.00 |
| S151 | S151 | B4 | Laboratory - Lavar | Lab | France | Ovary | Culex pipiens | MW56 | 33 | 29/08/2017 | run2 | True sample | 78 | italic(“Culex pipiens”) | Laboratory-Lavar | 22944 | FALSE | 0 | 0.00 |
| S152 | S152 | C4 | Laboratory - Lavar | Lab | France | Ovary | Culex pipiens | MW57 | 34 | 29/08/2017 | run2 | True sample | 79 | italic(“Culex pipiens”) | Laboratory-Lavar | 15082 | FALSE | 0 | 0.00 |
| S153 | S153 | D4 | Laboratory - Lavar | Lab | France | Ovary | Culex pipiens | MW58 | 35 | 29/08/2017 | run2 | True sample | 97 | italic(“Culex pipiens”) | Laboratory-Lavar | 17040 | FALSE | 0 | 0.00 |
| S154 | S154 | E4 | Laboratory - Lavar | Lab | France | Ovary | Culex pipiens | MW59 | 36 | 29/08/2017 | run2 | True sample | 76 | italic(“Culex pipiens”) | Laboratory-Lavar | 9626 | FALSE | 0 | 0.00 |
| S160 | S160 | K4 | Laboratory - Lavar | Lab | France | Ovary | Culex pipiens | MW60 | 37 | 29/08/2017 | run2 | True sample | 99 | italic(“Culex pipiens”) | Laboratory-Lavar | 72508 | FALSE | 0 | 0.00 |
| S162 | S162 | B5 | Laboratory - Lavar | Lab | France | Ovary | Culex pipiens | MW61 | 38 | 29/08/2017 | run2 | True sample | 90 | italic(“Culex pipiens”) | Laboratory-Lavar | 25180 | FALSE | 0 | 0.00 |
| S163 | S163 | L6 | Laboratory - Lavar | Lab | France | Ovary | Culex pipiens | MW62 | 39 | 30/08/2017 | run2 | True sample | 96 | italic(“Culex pipiens”) | Laboratory-Lavar | 12333 | FALSE | 0 | 0.00 |
| S164 | S164 | C5 | Laboratory - Lavar | Lab | France | Ovary | Culex pipiens | MW63 | 40 | 30/08/2017 | run2 | True sample | 74 | italic(“Culex pipiens”) | Laboratory-Lavar | 22368 | FALSE | 2 | 0.00 |
| S165 | S165 | D5 | Laboratory - Lavar | Lab | France | Ovary | Culex pipiens | MW64 | 41 | 30/08/2017 | run2 | True sample | 98 | italic(“Culex pipiens”) | Laboratory-Lavar | 17731 | FALSE | 4 | 0.00 |
| S166 | S166 | E5 | Field - Camping Europe | Field | France | Ovary | Culex pipiens | GL4 | 4 | 30/05/2017 | run2 | True sample | 53 | italic(“Culex pipiens”) | Field-Camping~Europe | 13979 | FALSE | 1 | 0.00 |
| S167 | S167 | F5 | Field - Bosc | Field | France | Ovary | Culex pipiens | J32 | 28 | 28/06/2017 | run2 | True sample | 59 | italic(“Culex pipiens”) | Field-Bosc | 14048 | FALSE | 2 | 0.00 |
| S169 | S169 | B7 | Field - Camping Europe | Field | France | Ovary | Culex pipiens | 5 | 43 | 16/05/2017 | run2 | True sample | 95 | italic(“Culex pipiens”) | Field-Camping~Europe | 11553 | FALSE | 0 | 0.00 |
| S170 | S170 | C7 | Field - Camping Europe | Field | France | Ovary | Culex pipiens | 6 | 44 | 16/05/2017 | run2 | True sample | 94 | italic(“Culex pipiens”) | Field-Camping~Europe | 8852 | FALSE | 0 | 0.00 |
| S18 | S18 | A1 | Laboratory - Lavar | Lab | France | Whole | Culex pipiens | MW75 | 0 | 30/08/2017 | run1 | True sample | 3 | italic(“Culex pipiens”) | Laboratory-Lavar | 4290 | FALSE | 0 | 0.00 |
| S19 | S19 | B1 | Laboratory - Lavar | Lab | France | Whole | Culex pipiens | MW65 | 0 | 30/08/2017 | run1 | True sample | 51 | italic(“Culex pipiens”) | Laboratory-Lavar | 44527 | FALSE | 0 | 0.00 |
| S20 | S20 | C1 | Laboratory - Lavar | Lab | France | Whole | Culex pipiens | MW66 | 0 | 30/08/2017 | run1 | True sample | 39 | italic(“Culex pipiens”) | Laboratory-Lavar | 42864 | FALSE | 6 | 0.00 |
| S21 | S21 | D1 | Laboratory - Lavar | Lab | France | Whole | Culex pipiens | MW67 | 0 | 30/08/2017 | run1 | True sample | 36 | italic(“Culex pipiens”) | Laboratory-Lavar | 33798 | FALSE | 3 | 0.00 |
| S22 | S22 | E1 | Laboratory - Lavar | Lab | France | Whole | Culex pipiens | MW68 | 0 | 30/08/2017 | run1 | True sample | 54 | italic(“Culex pipiens”) | Laboratory-Lavar | 19044 | FALSE | 2 | 0.00 |
| S23 | S23 | F1 | Laboratory - Lavar | Lab | France | Whole | Culex pipiens | MW69 | 0 | 30/08/2017 | run1 | True sample | 48 | italic(“Culex pipiens”) | Laboratory-Lavar | 38172 | FALSE | 0 | 0.00 |
| S24 | S24 | G1 | Laboratory - Lavar | Lab | France | Whole | Culex pipiens | MW70 | 0 | 30/08/2017 | run1 | True sample | 70 | italic(“Culex pipiens”) | Laboratory-Lavar | 42355 | FALSE | 8 | 0.00 |
| S25 | S25 | H1 | Laboratory - Lavar | Lab | France | Whole | Culex pipiens | MW71 | 0 | 30/08/2017 | run1 | True sample | 51 | italic(“Culex pipiens”) | Laboratory-Lavar | 47688 | FALSE | 0 | 0.00 |
| S26 | S26 | I1 | Laboratory - Lavar | Lab | France | Whole | Culex pipiens | MW72 | 0 | 30/08/2017 | run1 | True sample | 17 | italic(“Culex pipiens”) | Laboratory-Lavar | 5394 | FALSE | 0 | 0.00 |
| S27 | S27 | J1 | Laboratory - Lavar | Lab | France | Whole | Culex pipiens | MW73 | 0 | 30/08/2017 | run1 | True sample | 34 | italic(“Culex pipiens”) | Laboratory-Lavar | 24558 | FALSE | 0 | 0.00 |
| S28 | S28 | A2 | Laboratory - Lavar | Lab | France | Whole | Culex pipiens | MW74 | 0 | 30/08/2017 | run1 | True sample | 6 | italic(“Culex pipiens”) | Laboratory-Lavar | 4503 | FALSE | 0 | 0.00 |
| S30 | S30 | K1 | Laboratory - Lavar | Lab | France | Whole | Culex pipiens | MW1 | 0 | 23/08/2017 | run1 | True sample | 82 | italic(“Culex pipiens”) | Laboratory-Lavar | 25353 | FALSE | 4683 | 0.18 |
| S31 | S31 | L1 | Laboratory - Lavar | Lab | France | Whole | Culex pipiens | MW2 | 0 | 23/08/2017 | run1 | True sample | 44 | italic(“Culex pipiens”) | Laboratory-Lavar | 20417 | FALSE | 5214 | 0.26 |
| S32 | S32 | C2 | Laboratory - Lavar | Lab | France | Whole | Culex pipiens | MW3 | 0 | 23/08/2017 | run1 | True sample | 22 | italic(“Culex pipiens”) | Laboratory-Lavar | 12441 | FALSE | 2075 | 0.17 |
| S33 | S33 | D2 | Laboratory - Lavar | Lab | France | Whole | Culex pipiens | MW4 | 0 | 23/08/2017 | run1 | True sample | 26 | italic(“Culex pipiens”) | Laboratory-Lavar | 33867 | FALSE | 4362 | 0.13 |
| S34 | S34 | E2 | Laboratory - Lavar | Lab | France | Whole | Culex pipiens | MW5 | 0 | 23/08/2017 | run1 | True sample | 31 | italic(“Culex pipiens”) | Laboratory-Lavar | 9367 | FALSE | 764 | 0.08 |
| S35 | S35 | F2 | Laboratory - Lavar | Lab | France | Whole | Culex pipiens | MW6 | 0 | 23/08/2017 | run1 | True sample | 23 | italic(“Culex pipiens”) | Laboratory-Lavar | 11663 | FALSE | 8 | 0.00 |
| S36 | S36 | G2 | Laboratory - Lavar | Lab | France | Whole | Culex pipiens | MW7 | 0 | 23/08/2017 | run1 | True sample | 79 | italic(“Culex pipiens”) | Laboratory-Lavar | 33020 | FALSE | 2972 | 0.09 |
| S37 | S37 | H2 | Laboratory - Lavar | Lab | France | Whole | Culex pipiens | MW8 | 0 | 23/08/2017 | run1 | True sample | 88 | italic(“Culex pipiens”) | Laboratory-Lavar | 18340 | FALSE | 464 | 0.03 |
| S38 | S38 | I2 | Laboratory - Lavar | Lab | France | Whole | Culex pipiens | MW9 | 0 | 23/08/2017 | run1 | True sample | 63 | italic(“Culex pipiens”) | Laboratory-Lavar | 54790 | FALSE | 19 | 0.00 |
| S39 | S39 | J2 | Laboratory - Lavar | Lab | France | Whole | Culex pipiens | MW10 | 0 | 23/08/2017 | run1 | True sample | 75 | italic(“Culex pipiens”) | Laboratory-Lavar | 36273 | FALSE | 0 | 0.00 |
| S40 | S40 | K2 | Laboratory - Lavar | Lab | France | Whole | Culex pipiens | MW11 | 0 | 23/08/2017 | run1 | True sample | 83 | italic(“Culex pipiens”) | Laboratory-Lavar | 44448 | FALSE | 0 | 0.00 |
| S42 | S42 | A3 | Field - Camping Europe | Field | France | Whole | Culex pipiens | GLE1 | 0 | 30/05/2017 | run1 | True sample | 1 | italic(“Culex pipiens”) | Field-Camping~Europe | 4107 | FALSE | 0 | 0.00 |
| S43 | S43 | B3 | Field - Camping Europe | Field | France | Whole | Culex pipiens | GLE2 | 0 | 30/05/2017 | run1 | True sample | 11 | italic(“Culex pipiens”) | Field-Camping~Europe | 9279 | FALSE | 0 | 0.00 |
| S44 | S44 | C3 | Field - Camping Europe | Field | France | Whole | Culex pipiens | GLE3 | 0 | 30/05/2017 | run1 | True sample | 4 | italic(“Culex pipiens”) | Field-Camping~Europe | 8026 | FALSE | 29 | 0.00 |
| S45 | S45 | D3 | Field - Camping Europe | Field | France | Whole | Culex pipiens | GLE4 | 0 | 30/05/2017 | run1 | True sample | 13 | italic(“Culex pipiens”) | Field-Camping~Europe | 18150 | FALSE | 64 | 0.00 |
| S47 | S47 | F3 | Field - Camping Europe | Field | France | Whole | Culex pipiens | GLE6 | 0 | 30/05/2017 | run1 | True sample | 15 | italic(“Culex pipiens”) | Field-Camping~Europe | 1951 | FALSE | 0 | 0.00 |
| S48 | S48 | G3 | Field - Camping Europe | Field | France | Whole | Culex pipiens | GLE7 | 0 | 30/05/2017 | run1 | True sample | 60 | italic(“Culex pipiens”) | Field-Camping~Europe | 56738 | FALSE | 32 | 0.00 |
| S49 | S49 | H3 | Field - Bosc | Field | France | Whole | Culex pipiens | E1 | 0 | 28/06/2017 | run1 | True sample | 28 | italic(“Culex pipiens”) | Field-Bosc | 33498 | FALSE | 12 | 0.00 |
| S50 | S50 | I3 | Field - Bosc | Field | France | Whole | Culex pipiens | E2 | 0 | 28/06/2017 | run1 | True sample | 25 | italic(“Culex pipiens”) | Field-Bosc | 28481 | FALSE | 0 | 0.00 |
| S51 | S51 | J3 | Field - Bosc | Field | France | Whole | Culex pipiens | E3 | 0 | 28/06/2017 | run1 | True sample | 40 | italic(“Culex pipiens”) | Field-Bosc | 61788 | FALSE | 0 | 0.00 |
| S52 | S52 | K3 | Field - Bosc | Field | France | Whole | Culex pipiens | E4 | 0 | 28/06/2017 | run1 | True sample | 21 | italic(“Culex pipiens”) | Field-Bosc | 21553 | FALSE | 0 | 0.00 |
| S55 | S55 | B4 | Field - Bosc | Field | France | Whole | Culex pipiens | E6 | 0 | 28/06/2017 | run1 | True sample | 46 | italic(“Culex pipiens”) | Field-Bosc | 50447 | FALSE | 0 | 0.00 |
| S56 | S56 | C4 | Field - Bosc | Field | France | Whole | Culex pipiens | E7 | 0 | 28/06/2017 | run1 | True sample | 61 | italic(“Culex pipiens”) | Field-Bosc | 42609 | FALSE | 0 | 0.00 |
| S57 | S57 | D4 | Field - Bosc | Field | France | Whole | Culex pipiens | E8 | 0 | 28/06/2017 | run1 | True sample | 86 | italic(“Culex pipiens”) | Field-Bosc | 49157 | FALSE | 0 | 0.00 |
| S58 | S58 | E4 | Field - Bosc | Field | France | Whole | Culex pipiens | E9 | 0 | 28/06/2017 | run1 | True sample | 32 | italic(“Culex pipiens”) | Field-Bosc | 30357 | FALSE | 0 | 0.00 |
| S59 | S59 | F4 | Field - Bosc | Field | France | Whole | Culex pipiens | E10 | 0 | 28/06/2017 | run1 | True sample | 33 | italic(“Culex pipiens”) | Field-Bosc | 32798 | FALSE | 0 | 0.00 |
| S60 | S60 | G4 | Field - Bosc | Field | France | Whole | Culex pipiens | E11 | 0 | 28/06/2017 | run1 | True sample | 45 | italic(“Culex pipiens”) | Field-Bosc | 44485 | FALSE | 0 | 0.00 |
| S61 | S61 | H4 | Field - Bosc | Field | France | Whole | Culex pipiens | E12 | 0 | 28/06/2017 | run1 | True sample | 41 | italic(“Culex pipiens”) | Field-Bosc | 49545 | FALSE | 0 | 0.00 |
| S63 | S63 | J4 | Field - Bosc | Field | France | Whole | Culex pipiens | E14 | 0 | 28/06/2017 | run1 | True sample | 100 | italic(“Culex pipiens”) | Field-Bosc | 53444 | FALSE | 0 | 0.00 |
| S64 | S64 | K4 | Field - Bosc | Field | France | Whole | Culex pipiens | E15 | 0 | 28/06/2017 | run1 | True sample | 81 | italic(“Culex pipiens”) | Field-Bosc | 47628 | FALSE | 0 | 0.00 |
| S79 | S79 | B6 | Field - Camping Europe | Field | France | Ovary | Culex pipiens | J16 | 12 | 28/06/2017 | run1 | True sample | 68 | italic(“Culex pipiens”) | Field-Camping~Europe | 59755 | FALSE | 0 | 0.00 |
| S80 | S80 | C6 | Field - Camping Europe | Field | France | Ovary | Culex pipiens | J17 | 13 | 28/06/2017 | run1 | True sample | 83 | italic(“Culex pipiens”) | Field-Camping~Europe | 52788 | FALSE | 0 | 0.00 |
| S83 | S83 | F6 | Field - Camping Europe | Field | France | Ovary | Culex pipiens | J20 | 16 | 28/06/2017 | run1 | True sample | 73 | italic(“Culex pipiens”) | Field-Camping~Europe | 42272 | FALSE | 0 | 0.00 |
| S84 | S84 | G6 | Field - Camping Europe | Field | France | Ovary | Culex pipiens | J21 | 17 | 28/06/2017 | run1 | True sample | 49 | italic(“Culex pipiens”) | Field-Camping~Europe | 56676 | FALSE | 0 | 0.00 |
| S85 | S85 | H6 | Field - Camping Europe | Field | France | Ovary | Culex pipiens | J22 | 18 | 28/06/2017 | run1 | True sample | 35 | italic(“Culex pipiens”) | Field-Camping~Europe | 41690 | FALSE | 0 | 0.00 |
| S86 | S86 | I6 | Field - Camping Europe | Field | France | Ovary | Culex pipiens | J23 | 19 | 28/06/2017 | run1 | True sample | 80 | italic(“Culex pipiens”) | Field-Camping~Europe | 61984 | FALSE | 0 | 0.00 |
| S87 | S87 | J6 | Field - Bosc | Field | France | Ovary | Culex pipiens | J24 | 20 | 28/06/2017 | run1 | True sample | 58 | italic(“Culex pipiens”) | Field-Bosc | 65958 | FALSE | 0 | 0.00 |
| S88 | S88 | K6 | Field - Bosc | Field | France | Ovary | Culex pipiens | J25 | 21 | 28/06/2017 | run1 | True sample | 106 | italic(“Culex pipiens”) | Field-Bosc | 53102 | FALSE | 0 | 0.00 |
Taxonomic structure
Count
col <- brewer.pal(7, "Pastel2")
# reshape data for plot
test3 <- test %>% select(c(Sample, Species, Strain, Organ, Read_depth, Read_erwinia)) %>% reshape2::melt(id.vars=c("Sample", "Species", "Strain", "Organ"), vars=c("Read_depth", "Read_erwinia"))
count_whole <- test3[test3$Organ=="Whole",]
count_ovary <- test3[test3$Organ=="Ovary",]
make.italic <- function(x) as.expression(lapply(x, function(y) bquote(italic(.(y)))))
levels(count_whole$Species)= c("Aedes aegypti"=make.italic("Aedes aegypti"),
"Culex pipiens"=make.italic("Culex pipiens"),
"Culex quinquefasciatus"=make.italic("Culex quinquefasciatus"))
levels(count_ovary$Species)= c("Aedes aegypti"=make.italic("Aedes aegypti"),
"Culex pipiens"=make.italic("Culex pipiens"),
"Culex quinquefasciatus"=make.italic("Culex quinquefasciatus"))
levels(count_whole$Strain) <- c("Bosc", "Camping~Europe", "Guadeloupe", "Lavar~(lab)", expression(paste(italic("Wolbachia"), "- (Slab TC)")))
levels(count_ovary$Strain) <- c("Bosc", "Camping~Europe", "Guadeloupe", "Lavar~(lab)", expression(paste(italic("Wolbachia"), "- (Slab TC)")))
# plot
p_count1 <- ggplot(count_whole, aes(x = Sample, y = value, fill=variable))+
geom_bar(position = "dodge", stat = "identity")+
scale_fill_manual(values = col)+
theme_bw() +
theme(axis.text.x = element_text(angle = 90, size=12, hjust=1, vjust=0.5)) +
ggtitle("") +
guide_italics+
theme(legend.title = element_text(size = 20),
legend.position="bottom",
legend.text=element_text(size=14),
panel.spacing.y=unit(1, "lines"),
panel.spacing.x=unit(0.8, "lines"),
panel.spacing=unit(0,"lines"),
strip.background=element_rect(color="grey30", fill="grey90"),
strip.text.x = element_text(size = 16),
panel.border=element_rect(color="grey90"),
axis.ticks.x=element_blank(),
axis.text.y = element_text(size=18)) +
facet_wrap(~Species+Strain+Organ, scales = "free_x", ncol=3, labeller=label_parsed)+
labs(y="Sequence counts")+
ylim(0, 900000)+
geom_text(aes(label=value), position=position_dodge(width=1.1), width=0.25, size=4, hjust=-0.25, vjust=0.5, angle=90)+
guides(fill=guide_legend(title="Read"))## Warning: Ignoring unknown parameters: width
p_count2 <- ggplot(count_ovary, aes(x = Sample, y = value, fill=variable))+
geom_bar(position = "dodge", stat = "identity")+
scale_fill_manual(values = col)+
theme_bw() +
theme(axis.text.x = element_text(angle = 90, size=18, hjust=1, vjust=0.5)) +
ggtitle("") +
guide_italics+
theme(legend.title = element_text(size = 20),
legend.position="bottom",
legend.text=element_text(size=14),
panel.spacing.y=unit(1, "lines"),
panel.spacing.x=unit(0.8, "lines"),
panel.spacing=unit(0,"lines"),
strip.background=element_rect(color="grey30", fill="grey90"),
strip.text.x = element_text(size = 16),
panel.border=element_rect(color="grey90"),
axis.ticks.x=element_blank(),
axis.text.y = element_text(size=18)) +
facet_wrap(~Species+Strain+Organ, scales = "free_x", ncol=3, labeller=label_parsed)+
labs(y="Sequence counts")+
ylim(0, 900000)+
geom_text(aes(label=value), position=position_dodge(width=0.8), width=0.25, size=4, hjust=-0.25, vjust=0.5, angle=90)+
guides(fill=guide_legend(title="Read"))## Warning: Ignoring unknown parameters: width
## Warning: position_dodge requires non-overlapping x intervals
## Warning: position_dodge requires non-overlapping x intervals
## Warning: position_dodge requires non-overlapping x intervals
## Warning: position_dodge requires non-overlapping x intervals
## Warning: position_dodge requires non-overlapping x intervals
## Warning: position_dodge requires non-overlapping x intervals
# panels
p_group <- plot_grid(p_count1+theme(legend.position="none"),
p_count2+theme(legend.position="none"),
nrow=2,
ncol=1)+
draw_plot_label(c("B1", "B2"), c(0, 0), c(1, 0.5), size = 20)## Warning: position_dodge requires non-overlapping x intervals
## Warning: position_dodge requires non-overlapping x intervals
## Warning: position_dodge requires non-overlapping x intervals
## Warning: position_dodge requires non-overlapping x intervals
## Warning: position_dodge requires non-overlapping x intervals
## Warning: position_dodge requires non-overlapping x intervals
## Warning: position_dodge requires non-overlapping x intervals
## Warning: position_dodge requires non-overlapping x intervals
## Warning: position_dodge requires non-overlapping x intervals
## Warning: position_dodge requires non-overlapping x intervals
## Warning: position_dodge requires non-overlapping x intervals
## Warning: position_dodge requires non-overlapping x intervals
Whole (the most abundant nodes)
guide_italics <- guides(fill = guide_legend(label.theme = element_text(size = 16, face = "italic", colour = "Black", angle = 0),
nrow=2, byrow=TRUE))
# select whole
ps.filter.whole <- subset_samples(ps, Organ=="Whole")
ps.filter.whole <- prune_taxa(taxa_sums(ps.filter.whole) >= 1, ps.filter.whole)
ps.filter.whole <- prune_samples(sample_sums(ps.filter.whole) >= 1, ps.filter.whole)
ps.filter.whole## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 3 taxa and 33 samples ]
## sample_data() Sample Data: [ 33 samples by 19 sample variables ]
## tax_table() Taxonomy Table: [ 3 taxa by 1 taxonomic ranks ]
# data pour plot
#data_for_plot2 <- taxo_data_fast(ps.filter.whole, method = "abundance")
data_for_plot2 <- taxo_data(ps.filter.whole, top=15)## Warning in psmelt(ps_global): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
##
## 15 MOST ABUNDANT GENUS:
## "oligotype_AAGACTTA (40) | size:38025 / node_N0798 (40) | size:38213.",
## "oligotype_AAGACTTG (22) | size:4594 / node_N0802 (22) | size:4627.",
## "oligotype_TGAGTCGA (29) | size:7110 / node_N0311 (30) | size:8523.",
data_for_plot2$Name <- data_for_plot2$Name %>% gsub(pattern = "node_", replacement ="" ) %>% as.factor()
data_for_plot2$Name <- as.factor(data_for_plot2$Name)
new_names <- c("oligotype_AAGACTTA (40) | size:38025 / N0798 (40) | size:38213.",
"oligotype_TGAGTCGA (29) | size:7110 / N0311 (30) | size:8523.",
"oligotype_AAGACTTG (22) | size:4594 / N0802 (22) | size:4627.",
"Other.")
data_for_plot2$Name <- factor(data_for_plot2$Name, levels = new_names)
col_add <- brewer.pal(8, "Accent")
col <- c("oligotype_AAGACTTA (40) | size:38025 / N0798 (40) | size:38213."="#FFFFCF",
"oligotype_TGAGTCGA (29) | size:7110 / N0311 (30) | size:8523."="#FFE352",
"oligotype_AAGACTTG (22) | size:4594 / N0802 (22) | size:4627."="#F5F61B",
"Other."="#A0A0A0")
levels(data_for_plot2$Species)= c("Aedes aegypti"=make.italic("Aedes aegypti"),
"Culex pipiens"=make.italic("Culex pipiens"),
"Culex quinquefasciatus"=make.italic("Culex quinquefasciatus"))
levels(data_for_plot2$Strain) <- c("Bosc", "Camping~Europe", "Guadeloupe", "Lavar~(lab)", expression(paste(italic("Wolbachia"), "- (Slab TC)")))
#data_for_plot2 <- data_for_plot2 %>% na.omit()
p2 <- ggplot(data_for_plot2, aes(x = Sample, y = Relative_Abundance, fill = Name, species=Species, organ=Organ, Strain=Strain))+
geom_bar(position = "stack", stat = "identity")+
scale_fill_manual(values = col)+
theme_bw() +
theme(axis.text.x = element_text(angle = 90, size=18, hjust=1, vjust=0.5)) +
ggtitle("") +
guide_italics+
theme(legend.title = element_text(size = 20),
legend.position="bottom",
legend.text = element_text(size=14),
#legend.key.height = unit(1, 'cm'),
panel.spacing.y=unit(1, "lines"),
panel.spacing.x=unit(0.8, "lines"),
panel.spacing=unit(0,"lines"),
strip.background=element_rect(color="grey30", fill="grey90"),
strip.text.x = element_text(size = 16),
panel.border=element_rect(color="grey90"),
axis.ticks.x=element_blank(),
axis.text.y = element_text(size=18)) +
facet_wrap(~Species+Strain+Organ, scales = "free", ncol=3, labeller=label_parsed)+
labs(x="Sample", y="Relative abundance", fill="Oligotype / MED node")
p2Ovary (the most abundant nodes)
# select ovary
ps.filter.ovary <- subset_samples(ps, Organ=="Ovary")
ps.filter.ovary <- prune_taxa(taxa_sums(ps.filter.ovary) >= 1, ps.filter.ovary)
ps.filter.ovary <- prune_samples(sample_sums(ps.filter.ovary) >= 1, ps.filter.ovary)
ps.filter.ovary## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 1 taxa and 5 samples ]
## sample_data() Sample Data: [ 5 samples by 19 sample variables ]
## tax_table() Taxonomy Table: [ 1 taxa by 1 taxonomic ranks ]
## Warning in psmelt(ps_global): The sample variables:
## Sample
## have been renamed to:
## sample_Sample
## to avoid conflicts with special phyloseq plot attribute names.
##
## 15 MOST ABUNDANT GENUS:
## "oligotype_AAGACTTA (40) | size:38025 / node_N0798 (40) | size:38213.",
data_for_plot3$Name <- data_for_plot3$Name %>% gsub(pattern = "node_", replacement ="" ) %>% as.factor()
data_for_plot3$Name <- as.factor(data_for_plot3$Name)
levels(data_for_plot3$Species)= c("Culex pipiens"=make.italic("Culex pipiens"))
levels(data_for_plot3$Strain) <- c("Bosc", "Camping~Europe", "Lavar~(lab)")
p3 <- ggplot(data_for_plot3, aes(x = Sample, y = Relative_Abundance, fill = Name, species=Species, organ=Organ, Strain=Strain))+
geom_bar(position = "stack", stat = "identity")+
scale_fill_manual(values = col)+
theme_bw() +
theme(axis.text.x = element_text(angle = 90, size=18, hjust=1, vjust=0.5)) +
ggtitle("") +
guide_italics+
theme(legend.title = element_text(size = 20),
legend.position="bottom",
legend.text = element_text(size=14),
#legend.key.height = unit(1, 'cm'),
panel.spacing.y=unit(1, "lines"),
panel.spacing.x=unit(0.8, "lines"),
panel.spacing=unit(0,"lines"),
strip.background=element_rect(color="grey30", fill="grey90"),
strip.text.x = element_text(size = 16),
panel.border=element_rect(color="grey90"),
axis.ticks.x=element_blank(),
axis.text.y = element_text(size=18)) +
facet_wrap(~Species+Strain+Organ, scales = "free", ncol=3, labeller=label_parsed)+
labs(x="Sample", y="Relative abundance", fill="Oligotype / MED node")
p3# ps.filter.ovary@otu_table # only 1 oligotype
#
# a <- data.frame(ps.filter.ovary@sam_data)
# b <- data.frame(ps.filter.ovary@tax_table)
# count_table <- data.frame(ps.filter.ovary@otu_table)
#
# count_table %>%
# kbl() %>%
# kable_paper("hover", full_width = F)
#
# a$Relative_Abundance <- 1.0000000000
# a$Name <- paste0(b$ref,".")
#
# levels(a$Species)= c("Aedes aegypti"=make.italic("Aedes aegypti"),
# "Culex pipiens"=make.italic("Culex pipiens"),
# "Culex quinquefasciatus"=make.italic("Culex quinquefasciatus"))
#
# levels(a$Strain) <- c("Bosc", "Camping~Europe", "Guadeloupe", "Lavar~(lab)", expression(paste(italic("Wolbachia"), "- (Slab TC)")))
#
# p3 <- ggplot(a, aes(x = Sample, y = Relative_Abundance, fill = Name, species=Species, organ=Organ, Strain=Strain))+
# geom_bar(position = "stack", stat = "identity")+
# scale_fill_manual(values = "#FFFFCF")+
# theme_bw() +
# theme(axis.text.x = element_text(angle = 90)) +
# ggtitle("") +
# guide_italics+
# theme(legend.title = element_text(size = 20),
# legend.position="bottom",
# legend.text = element_text(size=14),
# #legend.key.height = unit(1, 'cm'),
# panel.spacing.y=unit(1, "lines"),
# panel.spacing.x=unit(0.8, "lines"),
# panel.spacing=unit(0,"lines"),
# strip.background=element_rect(color="grey30", fill="grey90"),
# strip.text.x = element_text(size = 16),
# panel.border=element_rect(color="grey90"),
# axis.ticks.x=element_blank(),
# axis.text.y = element_text(size=18)) +
# facet_wrap(~Species+Strain+Organ, scales = "free", ncol=3, labeller=label_parsed)+
# labs(x="Sample", y="Relative abundance", fill="Oligotype / MED Node")
#
# p3Panels taxonomy of whole / ovary
legend_plot <- get_legend(p2 + theme(legend.position="bottom"))
# panels
p_group <- plot_grid(p2+theme(legend.position="none"),
p3+theme(legend.position="none"),
nrow=2,
ncol=1)+
draw_plot_label(c("A1", "A2"), c(0, 0), c(1, 0.5), size = 20)
p_taxo <- plot_grid(p_group, legend_plot, nrow=2, rel_heights = c(1, .1))
p_taxoSave taxonomic plot
setwd(path_plot)
tiff("2De_OLIGO_counts_erwinia.tiff", units="in", width=20, height=18, res=300)
p_counts
dev.off()## quartz_off_screen
## 2
tiff("2De_OLIGO_taxonomic_erwinia_whole.tiff", units="in", width=16, height=12, res=300)
p2
dev.off()## quartz_off_screen
## 2
tiff("2De_OLIGO_taxonomic_erwinia_ovary.tiff", units="in", width=18, height=14, res=300)
p3
dev.off()## quartz_off_screen
## 2
## quartz_off_screen
## 2
png("2De_OLIGO_counts_erwinia_big.png", units="in", width=20, height=18, res=300)
p_counts
dev.off()## quartz_off_screen
## 2
png("2De_OLIGO_counts_erwinia_small.png", units="in", width=18, height=14, res=300)
p_counts
dev.off()## quartz_off_screen
## 2
## quartz_off_screen
## 2
## quartz_off_screen
## 2
png("2De_OLIGO_taxonomic_erwinia_big.png", units="in", width=18, height=18, res=300)
p_taxo
dev.off()## quartz_off_screen
## 2
png("2De_OLIGO_taxonomic_erwinia_small.png", units="in", width=18, height=14, res=300)
p_taxo
dev.off()## quartz_off_screen
## 2
Make main plot
setwd(paste0(path_oligo,"/erwinia/oligotyping_Erwinia_sequences-c8-s1-a0.0-A0-M10/HTML-OUTPUT"))
img <- magick::image_read("entropy.png")
p_entropy <- magick::image_ggplot(img, interpolate = TRUE)
p_entropy+ theme(plot.margin = unit(c(-7,-2.5,-7,-0.5), "cm"))p_entropy2 <- plot_grid(p_entropy, nrow=1)+
draw_plot_label(c("C"), c(0), c(1), size=20, hjust=-0.5)
p_entropy2setwd(path_plot)
tiff("2De_OLIGO_main_erwinia.tiff", width=36, height=36, res=300, units="in")
t_plot
dev.off()## quartz_off_screen
## 2
## quartz_off_screen
## 2